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Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response

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Abstract

Microorganisms dwell in diverse plant niches as non-axenic biotic components that are beneficial as well pathogenic for the host. They improve nutrients-uptake, stress tolerance, phytohormone synthesis, and strengthening the defense system through phyllosphere, rhizosphere, and endosphere. The negative consequences of the microbial communities are largely in the form of diseases characterized by certain symptoms such as gall, cankers, rots etc. Uncultivable and unspecified nature of different phytomicrobiomes communities is a challenge in the management of plant disease, a leading cause for the loss of the plant products. Metagenomics has opened a new gateway for the exploration of microorganisms that are hitherto unknown, enables investigation of the functional aspect of microbial gene products through metatranscriptomics and metabolomics. Metagenomics offers advantages of characterizing previously unknown microorganisms from extreme environments like hot springs, glaciers, deep seas, animal gut etc. besides bioprospecting gene products such as Taq polymerase, bor encoded indolotryptoline, hydrolases, and polyketides. This review provides a detailed account of the phytomicrobiome networks and highlights the importance and limitations of metagenomics and other meta-omics approaches for the understanding of plant microbial diversity with special focus on the disease control and its management.

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Acknowledgements

Authors would like to acknowledge authorities of Lovely Professional University.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

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Author notes

  1. Prachi Kakade

    Present address: Department of Botany, D. P. Bhosale College, Koregaon, , Satara, 415501, Maharashtra, India

Authors and Affiliations

  1. School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India

    Atif Khurshid Wani, Nahid Akhtar, Reena Singh & Chirag Chopra

  2. Department of Botany, Amdar Shashikant Shinde Mahavidyalay, 415012, Medha, Satara, India

    Prachi Kakade & Saurabha B. Zimare

  3. Department of Botany, Savitribai Phule Pune University, 411007, Pune, India

    Mahesh Borde

  4. Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, 31982, Al- Ahsa, Saudi Arabia

    Jameel M. Al-Khayri

  5. Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, 400094, Mumbai, India

    Penna Suprasanna

  6. Department of Botany, D. P. Bhosale College, Koregaon, , Satara, 415501, Maharashtra, India

    Saurabha B. Zimare

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Wani, A.K., Akhtar, N., Singh, R. et al. Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response. Mol Biol Rep 49, 12165–12179 (2022). https://doi.org/10.1007/s11033-022-07936-7

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